H. Adakal, D. Meyer, C. Carasco-lacombe, V. Pinarello, F. Allè-gre et al., MLST scheme of Ehrlichia ruminantium: Genomic stasis and recombination in strains from Burkina-Faso, Infection, Genetics and Evolution, vol.9, issue.6, pp.1320-1328, 2009.
DOI : 10.1016/j.meegid.2009.08.003

H. Adakal, L. Gavotte, F. Stachurski, M. Konkobo, H. Henri et al., Clonal origin of emerging populations of Ehrlichia ruminantium in Burkina Faso, Infection, Genetics and Evolution, vol.10, issue.7, pp.903-912, 2010.
DOI : 10.1016/j.meegid.2010.05.011
URL : https://hal.archives-ouvertes.fr/hal-00539294

N. Ahmed, S. M. Dev, D. L. Valverde, P. Vijayachar, R. S. Machang-'u et al., Multilocus sequence typing method for identification and genotypic classification of pathogenic Leptospira species, Ann. Clin. Microbiol . Antimicrob, vol.5, issue.28, pp.10-1186, 2006.

M. T. Allsopp and B. A. Allsopp, Extensive genetic recombination occurs in the field between different genotypes of Ehrlichia ruminantium, Veterinary Microbiology, vol.124, issue.1-2, pp.58-65, 2007.
DOI : 10.1016/j.vetmic.2007.03.012

M. T. Allsopp, H. Van-heerden, H. C. Steyn, and B. A. Allsopp, Isolates, Annals of the New York Academy of Sciences, vol.29, issue.1, pp.685-691, 2003.
DOI : 10.1111/j.1749-6632.2003.tb07444.x

S. D. Blacksell, R. Luksameetanasan, T. Kalambaheti, N. Aukkanit, D. H. Paris et al., isolates causing human scrub typhus at two sites in north-eastern and western Thailand, FEMS Immunology & Medical Microbiology, vol.52, issue.3, pp.335-342, 2008.
DOI : 10.1111/j.1574-695X.2007.00375.x

S. Chattopadhyay and A. L. Richards, Scrub Typhus Vaccines: Past History and Recent Developments, Human Vaccines, vol.3, issue.3, pp.73-80, 2007.
DOI : 10.4161/hv.3.3.4009

N. H. Cho, H. R. Kim, J. H. Lee, S. Y. Kim, J. Kim et al., The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host cell interaction genes, Proc. Natl. Acad. Sci. U.S.A. 104, pp.7981-7986, 2007.
DOI : 10.1073/pnas.0611553104

R. E. Coleman, T. Monkanna, K. J. Linthicum, D. A. Strickman, S. P. Frances et al., Occurrence of Orientia tsutsugamushi in small mammals from Thailand, Am. J. Trop. Med. Hyg, vol.69, pp.519-524, 2003.

A. C. Darby, N. H. Cho, H. H. Fuxelius, J. Westberg, and S. G. Andersson, Intracellular pathogens go extreme: genome evolution in the Rickettsiales, Trends in Genetics, vol.23, issue.10, pp.511-520, 2007.
DOI : 10.1016/j.tig.2007.08.002

J. Engelstä-der and A. Telshow, Cytoplasmic incompatibility and host population structure, Heredity, vol.54, issue.3, pp.196-207, 2009.
DOI : 10.1073/pnas.0403853101

S. P. Frances, P. Watcharapichat, D. Phulsuksombati, and P. Tanskul, Transmission of Orientia tsutsugamushi, the aetiological agent for scrub typhus, to co-feeding mites, Parasitology, vol.120, issue.6, pp.601-607, 2000.
DOI : 10.1017/S0031182099005909

S. P. Frances, P. Watcharapichat, and D. Phusuksombati, (Acari: Trombiculidae), Journal of Medical Entomology, vol.38, issue.1, pp.17-21, 2001.
DOI : 10.1603/0022-2585-38.1.17

Y. X. Fu, Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, vol.147, pp.915-925, 1997.

Y. X. Fu and W. H. Li, Statistical tests of neutrality of mutations, Genetics, vol.133, pp.693-709, 1993.

H. H. Fuxelius, A. Darby, C. K. Min, N. H. Cho, and S. G. Andersson, The genomic and metabolic diversity of Rickettsia, Research in Microbiology, vol.158, issue.10, pp.745-753, 2007.
DOI : 10.1016/j.resmic.2007.09.008

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

T. A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser, vol.41, pp.95-98, 1999.

H. Harbottle, D. G. White, P. F. Mcdermott, R. D. Walker, and S. Zhao, Comparison of Multilocus Sequence Typing, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Typing for Characterization of Salmonella enterica Serotype Newport Isolates, Journal of Clinical Microbiology, vol.44, issue.7, pp.2449-2457, 2006.
DOI : 10.1128/JCM.00019-06

W. G. Hill and A. Robertson, Linkage disequilibrium in finite populations, Theoretical and Applied Genetics, vol.19, issue.6, pp.226-231, 1968.
DOI : 10.1007/BF01245622

H. Inokuma, P. Brouqui, M. Drancourt, and D. Raoult, Citrate Synthase Gene Sequence: a New Tool for Phylogenetic Analysis and Identification of Ehrlichia, Journal of Clinical Microbiology, vol.39, issue.9, pp.3031-3039, 2001.
DOI : 10.1128/JCM.39.9.3031-3039.2001

T. H. Jukes and C. R. Cantor, Evolution of Protein Molecules, Mammalian Protein Metabolism, pp.21-132, 1969.
DOI : 10.1016/B978-1-4832-3211-9.50009-7

J. K. Kelly, A test of neutrality based on interlocus associations, Genetics, vol.146, pp.1197-1206, 1997.

M. Kimura, The Neutral Theory of Molecular Evolution, 1983.

L. Klasson and S. G. Andersson, Evolution of minimal-gene-sets in host-dependent bacteria, Trends in Microbiology, vol.12, issue.1, pp.37-43, 2004.
DOI : 10.1016/j.tim.2003.11.006

S. Kurtz, A. Phillippy, A. L. Delcher, M. Smoot, M. Shumway et al., Versatile and open software for comparing large genomes, 2004.

K. Lerdthusnee, N. Khlaimanee, T. Monkanna, N. Sangjun, S. Mungviriya et al., to Laboratory Mice, Journal of Medical Entomology, vol.39, issue.3, pp.521-525, 2002.
DOI : 10.1603/0022-2585-39.3.521

P. Librado and J. Rozas, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, vol.25, issue.11, pp.1451-1452, 2009.
DOI : 10.1093/bioinformatics/btp187

R. L. Mccombie, R. A. Finkelstein, and D. E. Wood, Multilocus Sequence Typing of Historical Burkholderia pseudomallei Isolates Collected in Southeast Asia from 1964 to 1967 Provides Insight into the Epidemiology of Melioidosis, Journal of Clinical Microbiology, vol.44, issue.8, pp.2951-2962, 2006.
DOI : 10.1128/JCM.00725-06

M. P. Mcleod, Q. Xiang, S. E. Karpathy, J. Gioia, S. K. Highlander et al., Complete Genome Sequence of Rickettsia typhi and Comparison with Sequences of Other Rickettsiae, Journal of Bacteriology, vol.186, issue.17, pp.5842-5855, 2004.
DOI : 10.1128/JB.186.17.5842-5855.2004

N. A. Moran and A. Mira, The process of genome shrinkage in the obligate symbiont Buchnera aphidicola, Genome Biol, vol.2, pp.54-55, 2001.

N. A. Moran and G. R. Plague, Genomic changes following host restriction in bacteria, Current Opinion in Genetics & Development, vol.14, issue.6, pp.627-633, 2004.
DOI : 10.1016/j.gde.2004.09.003

K. Nakayama, A. Yamashita, K. Kurokawa, T. Morimoto, M. Ogawa et al., The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During Reductive Genome Evolution, DNA Research, vol.15, issue.4, pp.185-199, 2008.
DOI : 10.1093/dnares/dsn011

M. Nei, Molecular Evolutionary Genetics, 1987.

M. Nei and T. Gojobori, Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions, Mol. Biol. Evol, vol.3, pp.418-426, 1986.

D. H. Paris, N. Aukkanit, K. Jenjaroen, S. D. Blacksell, and N. P. Day, A highly sensitive quantitative real-time PCR assay based on the groEL gene of contemporary Thai strains of Orientia tsutsugamushi, Clinical Microbiology and Infection, vol.15, issue.5, pp.488-495, 2009.
DOI : 10.1111/j.1469-0691.2008.02671.x

S. Phasomkusolsil, P. Tanskul, S. Ratanatham, P. Watchrapichat, D. Phulsuksombati et al., (Acari: Trombiculidae), Journal of Medical Entomology, vol.46, issue.6, pp.1442-1445, 2009.
DOI : 10.1603/033.046.0628

D. Posada, jModelTest: Phylogenetic Model Averaging, Molecular Biology and Evolution, vol.25, issue.7, pp.1253-1256, 2008.
DOI : 10.1093/molbev/msn083

S. Rozen and H. J. Skaletsky, Primer3 on the WWW for General Users and for Biologist Programmers, Bioinformatics Methods and Protocols: Methods in Molecular Biology, pp.365-386, 2000.
DOI : 10.1385/1-59259-192-2:365

B. Sallstrom and S. G. Andersson, Genome reduction in the ??-Proteobacteria, Current Opinion in Microbiology, vol.8, issue.5, pp.579-585, 2005.
DOI : 10.1016/j.mib.2005.08.002

S. Y. Seong, M. K. Kim, S. M. Lee, Z. Odgerel, M. S. Choi et al., Neutralization epitopes on the antigenic domain II of the Orientia tsutsugamushi 56-kDa protein revealed by monoclonal antibodies, Vaccine, vol.19, issue.1, pp.2-9, 2000.
DOI : 10.1016/S0264-410X(00)00167-5

S. Y. Seong, M. S. Huh, W. J. Jang, S. G. Park, J. G. Kim et al., Induction of homologous immune response to Rickettsia tsutsugamushi Boryong with a partial 56-kilodalton recombinant antigen fused with the maltose-binding protein MBP-Bor56, Infect. Immun, vol.65, pp.1541-1545, 1997.

P. Sonthayanon, W. Chierakul, V. Wuthiekanun, K. Phimda, S. Pukrittayakamee et al., Association of High Orientia tsutsugamushi DNA Loads with Disease of Greater Severity in Adults with Scrub Typhus, Journal of Clinical Microbiology, vol.47, issue.2, pp.430-434, 2009.
DOI : 10.1128/JCM.01927-08

P. Sonthayanon, S. J. Peacock, W. Chierakul, V. Wuthiekanun, S. D. Blacksell et al., High Rates of Homologous Recombination in the Mite Endosymbiont and Opportunistic Human Pathogen Orientia tsutsugamushi, PLoS Neglected Tropical Diseases, vol.31, issue.7, 2010.
DOI : 10.1371/journal.pntd.0000752.s001

C. K. Stover, D. P. Marana, J. M. Carter, B. A. Roe, E. Mardis et al., The 56- kilodalton major protein antigen of Rickettsia tsutsugamushi: molecular cloning and sequence analysis of the sta56 gene and precise identification of a strainspecific epitope, Infect. Immun, vol.58, pp.2076-2084, 1990.

C. Suttinont, K. Losuwanaluk, K. Niwatayakul, S. Hoontrakul, W. Intaranongpai et al., Causes of acute, undifferentiated, febrile illness in rural Thailand: results of a prospective observational study, Annals of Tropical Medicine & Parasitology, vol.68, issue.4, pp.363-370, 2006.
DOI : 10.1097/00001432-200310000-00009

F. Tajima, Statistical method for testing the neutral mutationhypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

M. Takahashi, M. Murata, E. Hori, H. Tanaka, and A. Kawamura, Transmission of Rickettsia tsutsugamushi from Apodemus speciosus, a wild rodent, to larval trombiculid mites during the feeding process, Jpn. J. Exp. Med, vol.60, pp.203-208, 1990.

M. Takahashi, M. Murata, H. Misumi, E. Hori, A. Kawamura-jr et al., Failed Vertical Transmission of Rickettsia tsutsugamushi (Rickettsiales: Rickettsiaceae) Acquired from Rickettsemic Mice by Leptotrombidium pallidum (Acari: Trombiculidae), Journal of Medical Entomology, vol.31, issue.2, pp.212-216, 1994.
DOI : 10.1093/jmedent/31.2.212

I. Tamas, L. Klasson, B. Canback, A. K. Naslund, A. S. Eriksson et al., 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria, Science, vol.296, issue.5577, pp.2376-2379, 2002.
DOI : 10.1126/science.1071278

J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, vol.25, issue.24, pp.4876-4882, 1997.
DOI : 10.1093/nar/25.24.4876

R. Traub, W. Jr, C. L. Jones, M. R. O-'keefe, and J. J. , THE ACQUISITION OF RICKETTSIA TSUTSUGAMUSHI BY CHIGGERS (TROMBICULID MITES) DURING THE FEEDING PROCESS, Annals of the New York Academy of Sciences, vol.24, issue.1, pp.91-114, 1975.
DOI : 10.1016/0014-4894(63)90019-5

R. Urwin and M. C. Maiden, Multi-locus sequence typing: a tool for global epidemiology, Trends in Microbiology, vol.11, issue.10, pp.479-487, 2003.
DOI : 10.1016/j.tim.2003.08.006

J. D. Wall, Recombination and the power of statistical tests of neutrality, Genetical Research, vol.74, issue.1, pp.65-69, 1999.
DOI : 10.1017/S0016672399003870

G. A. Watterson, On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975.
DOI : 10.1016/0040-5809(75)90020-9

G. Watt and P. Parola, Scrub typhus and tropical rickettsioses, Current Opinion in Infectious Diseases, vol.16, issue.5, pp.429-436, 2003.
DOI : 10.1097/00001432-200310000-00009